Do I need to run LD Prune before running ADMIXTOOLS 2? - Githubissues

uqrmaie1 / admixtools

https://uqrmaie1.github.io/admixtools

74 stars 14 forks source link

Do I need to run LD Prune before running ADMIXTOOLS 2? #42

Open maruiqi0710 opened 1 year ago

maruiqi0710 commented 1 year ago

Do I need to run LD Prune before running ADMIXTOOLS 2?

uqrmaie1 commented 1 year ago

It's generally not necessary to do LD pruning before running ADMIXTOOLS 2. The block jackknife method used for computing standard errors accounts for correlations between nearby SNPs. However, LD pruning might help in speeding things up and reducing the memory footprint.